Merge pull request #100 from PhysiCell-Tools/development

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PhysiCell-Tools · Jun 18, 2023 · 9bf10d0 · 9bf10d0
2 parents 0de1bf8 + a55e365
commit 9bf10d0
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Showing 4 changed files with 35 additions and 21 deletions.
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-2.26.3
+2.26.4
diff --git a/bin/ics_tab.py b/bin/ics_tab.py
@@ -935,15 +935,19 @@ def hex_pts_box(self):
                 for xval in np.arange(x_min,x_max, x_spacing):
                     # xval_offset = xval + (y_idx%2) * self.cell_radius
                     xval_offset = self.x0_value + xval + (y_idx%2) * self.cell_radius
-
-                    xlist.append(xval_offset)
                     yval_offset = yval + self.y0_value
-                    ylist.append(yval_offset)
-                    # self.csv_array = np.append(self.csv_array,[[xval,yval,zval, cell_type_index]],axis=0)
-                    self.csv_array = np.append(self.csv_array,[[xval_offset,yval_offset, zval, cell_type_index]],axis=0)
-                    rlist.append(rval)
-                    self.cell_radii.append(self.cell_radius)
-                    count+=1
+
+                    if xval_offset < self.plot_xmin or xval_offset > self.plot_xmax \
+                        or yval_offset < self.plot_ymin or yval_offset > self.plot_ymax:
+                        continue
+                    else:
+                        xlist.append(xval_offset)
+                        ylist.append(yval_offset)
+                        # self.csv_array = np.append(self.csv_array,[[xval,yval,zval, cell_type_index]],axis=0)
+                        self.csv_array = np.append(self.csv_array,[[xval_offset,yval_offset, zval, cell_type_index]],axis=0)
+                        rlist.append(rval)
+                        self.cell_radii.append(self.cell_radius)
+                        count+=1
         else:   # 3D
 
             # for z in np.arange(z_min, z_max, z_spacing):
@@ -1072,14 +1076,19 @@ def hex_pts_annulus(self):
                 #     # plt.plot(xval_offset,yval,'ro',markersize=30)
 
                     xval_offset += self.x0_value
-                    xlist.append(xval_offset)
                     yval_offset = yval + self.y0_value
-                    ylist.append(yval_offset)
-                    # self.csv_array = np.append(self.csv_array,[[xval_offset,yval,zval, cell_type_index]],axis=0)
-                    self.csv_array = np.append(self.csv_array,[[xval_offset,yval_offset,zval, cell_type_index]],axis=0)
-                    rlist.append(rval)
-                    self.cell_radii.append(self.cell_radius)
-                    count+=1
+
+                    if xval_offset < self.plot_xmin or xval_offset > self.plot_xmax \
+                        or yval_offset < self.plot_ymin or yval_offset > self.plot_ymax:
+                        continue
+                    else:
+                        xlist.append(xval_offset)
+                        ylist.append(yval_offset)
+                        # self.csv_array = np.append(self.csv_array,[[xval_offset,yval,zval, cell_type_index]],axis=0)
+                        self.csv_array = np.append(self.csv_array,[[xval_offset,yval_offset,zval, cell_type_index]],axis=0)
+                        rlist.append(rval)
+                        self.cell_radii.append(self.cell_radius)
+                        count+=1
 
         self.numcells_l.append(count)
 

diff --git a/bin/populate_tree_cell_defs.py b/bin/populate_tree_cell_defs.py
@@ -41,9 +41,9 @@ def validate_cell_defs(cell_defs_elm, skip_validate):
         if skip_validate:
             logging.debug(f'Continuing in spite of these missing elements.')
         else:
-            # logging.debug(f'\n A configuration file (.xml) for the PMB needs to explicitly \nprovide all required parameters for each <cell_definition>.\nIt cannot use the legacy hierarchical format where only\n partial parameters are provided and the rest are inherited from a parent.")
+            # logging.debug(f'\n A configuration file (.xml) for the Studio needs to explicitly \nprovide all required parameters for each <cell_definition>.\nIt cannot use the legacy hierarchical format where only\n partial parameters are provided and the rest are inherited from a parent.")
             warn_user = """
-            A configuration file (.xml) for the PMB needs to explicitly 
+            A configuration file (.xml) for the Studio needs to explicitly 
             provide all required parameters for each <cell_definition>.
             It cannot use the legacy hierarchical format where only 
             partial parameters are provided and the rest are inherited from a parent.

diff --git a/bin/rules_tab.py b/bin/rules_tab.py
@@ -1972,11 +1972,16 @@ def fill_gui(self):
             #     print(f'{full_rules_fname} is not a valid file')
             #     logging.error(f'{full_rules_fname} is not a valid file')
 
+        # if no rules are defined in the .xml, set default folder, file and enable them in the tab
         else:  # should empty the Rules tab
             # self.rules_text.setPlainText("")
-            self.rules_folder.setText("")
-            self.rules_file.setText("")
-            self.rules_enabled.setChecked(False)
+            # self.rules_folder.setText("")
+            # self.rules_file.setText("")
+            # self.rules_enabled.setChecked(False)
+            self.rules_folder.setText("config")
+            self.rules_file.setText("rules.csv")
+            self.rules_enabled.setChecked(True)
+
             # self.rules_table.clear()  # NO, this is not the droid you're looking for
             self.clear_rules()
         return